Chromobacterium violaceum is a Gram-negative, facultativeanaerobic, non-sporing coccobacillus. It is motile with the help of a single flagellum which is located at the pole of the coccobacillus. Usually, there are one or two more lateral flagella as well,[1] it is part of the normal flora of water and soil of tropical and sub-tropical regions of the world. It produces a natural antibiotic called violacein, which may be useful for the treatment of colon and other cancers,[2] it grows readily on nutrient agar, producing distinctive smooth low convex colonies with a dark violet metallic sheen (due to violacein production).[3] Some strains of the bacteria which do not produce this pigment have also been reported,[4] it has the ability to break down tarballs.[5]

C. violaceum rarely infects humans, but when it does it causes skin lesions, sepsis, and liver abscesses that may be fatal.[7] The first reported case of Chromobacterium violaceum infection in humans in literature is from Malaysia in 1927.[1] Only 150 cases have been reported in literature since then.[8] To date, cases have been reported from Argentina, Australia, Brazil, Cuba, India, Japan, Nigeria, Singapore, Sri Lanka, Taiwan, United States and Vietnam, the commonest mode of entry of the bacteria into the body is through the injured skin coming in contact with soil or water containing the bacteria.[1][9] The disease usually starts as a limited infection of the skin at the point of entry of the bacteria, which progresses to necrotizing metastatic lesions, then multiple abscesses of the liver, lung, spleen, skin, lymph nodes or brain, leading to severe septicaemia, culminating in multiorgan failure which may be fatal.[10] Other reported pathologies include chronic granulomatosis, osteomyelitis, cellulitis, diarrhoea, septic spondylitis, conjunctivitis, periorbital and ocular infection.[1][11][12][13][14] Care must be taken because Burkholderia pseudomallei is commonly misidentified as C. violaceum by many common identification methods.[15][16] The two are readily distinguished because B. pseudomallei produces large wrinkled colonies, whereas C. violaceum produces a distinctive violet pigment.

1.
Janthinobacterium lividum
–
Janthinobacterium lividum is an aerobic, gram-negative, soil-dwelling bacterium that has a distinctive dark-violet color. This color is due to a compound called violacein, which is produced when glycerol is metabolized as a carbon source, violacein has anti-bacterial, anti-viral, and anti-fungal properties. The genus name, Janthinobacterium, comes from Latin janthinus, which means violet or violet-blue + bacterium, the species name is also from Latin, lividum, which means of a blue or leaden color. This bacterium produces antifungal compounds, such as indole-3-carboxaldehyde and violacein, J. lividum inhibits the toxic effect and growth of a fungus known as Batrachochytrium. A study conducted in 2009 explored the effects of Bd and the use of J. lividium in the lab for survival. They used three experimental treatments, frogs infected with Bd, frogs given the bacteria J. lividium and frogs with the given bacteria, nearly all of the frogs exposed to Bd experienced mortality while none of the other treatments had any deaths. This effectively introduced the use of J. lividium as a method for Bd prevention in the lab setting. Type strain of Janthinobacterium lividum at BacDive - the Bacterial Diversity Metadatabase

2.
Agar plate
–
An agar plate is a Petri dish that contains a growth medium used to culture microorganisms or small plants like the moss Physcomitrella patens. Selective growth compounds may also be added to the media, such as antibiotics, individual microorganisms placed on the plate will grow into individual colonies, each a clone genetically identical to the individual ancestor organism. Some commonly used agar plate types are, Blood agar plates contain mammalian blood, bAPs are enriched, differential media used to isolate fastidious organisms and detect hemolytic activity. β-Hemolytic activity will show lysis and complete digestion of red blood cell contents surrounding a colony, α-Hemolysis will only cause partial lysis of the red blood cells and will appear green or brown, due to the conversion of hemoglobin to methemoglobin. An example of this would be Streptococcus viridans, γ-Hemolysis is the term referring to a lack of hemolytic activity. BAPs also contain meat extract, tryptone, sodium chloride, chocolate agar is a type of blood agar plate in which the blood cells have been lysed by heating the cells to 56 °C. It is used for growing fastidious respiratory bacteria, such as Haemophilus influenzae, no chocolate is actually contained in the plate, it is named for the coloration only. Horse blood agar is a type of blood-enriched microbiological culture media, as it is enriched, it allows the growth of certain fastidious bacteria, and allows indication of haemolytic activity in these bacterial cultures. Thayer-Martin agar is a chocolate agar designed to isolate Neisseria gonorrhoeae, thiosulfate-citrate-bile salts-sucrose agar enhances growth of Vibrio spp. including Vibrio cholerae. Granada medium is used to isolate and differentiate group B Streptococcus, Streptococcus agalactiae from clinical samples and it grows in Granada medium as red colonies and most of accompanying bacteria are inhibited. Hektoen enteric agar is designed to isolate and recover fecal bacteria belonging to the Enterobacteriaceae family and it is particularly useful in isolating Salmonella and Shigella. Lysogeny broth MacConkey agar is a selective and differential medium used to differentiate between Gram-negative bacteria while inhibiting the growth of Gram-positive bacteria, the addition of bile salts and crystal violet to the agar inhibits the growth of most Gram-positive bacteria, making MacConkey agar selective. Lactose and neutral red are added to differentiate the lactose fermenters, an alternative medium, eosin methylene blue serves a similar purpose. Mannitol salt agar is also a selective and differential medium, the mannitol indicates organisms that ferment mannitol, mannitol fermentation produces lactic acid, lowering the pH and turning the plate yellow. The salt is to select for halophiles, organisms that cannot withstand a high salt content are unable to grow well, mueller-Hinton agar contains beef infusion, peptone, and starch, and is used primarily for antibiotic susceptibility testing. It can be in a form of blood agar, nutrient agar is usually used for growth of nonfastidious organisms and observation of pigment production. It is safe to use in science laboratories because it does not selectively grow pathogenic bacteria. Önöz agar allows more rapid bacteriological diagnosis, as Salmonella and Shigella colonies can be clearly and reliably differentiated from other Enterobacteriaceae, the yields of Salmonella from stool samples obtained, when using this medium, are higher than those obtained with LEIFSON agar or Salmonella–Shigella agar

3.
Centers for Disease Control and Prevention
–
The Centers for Disease Control and Prevention is the leading national public health institute of the United States. The CDC is a United States federal agency under the Department of Health and Human Services, headquartered near Atlanta and its main goal is to protect public health and safety through the control and prevention of disease, injury, and disability in the US and internationally. The CDC focuses national attention on developing and applying disease control, the Communicable Disease Center was founded July 1,1946, as the successor to the World War II Malaria Control in War Areas program of the Office of National Defense Malaria Control Activities. Preceding its founding, organizations with global influence in malaria control were the Malaria Commission of the League of Nations, the Rockefeller Foundation greatly supported malaria control, sought to have the governments take over some of its efforts, and collaborated with the agency. The new agency was a branch of the U. S, Public Health Service and Atlanta was chosen as the location because malaria was endemic in the Southern United States. The agency changed names before adopting the name Communicable Disease Center in 1946, Offices were located on the sixth floor of the Volunteer Building on Peachtree Street. Among its 369 employees, the jobs at CDC were originally entomology. In CDCs initial years, more than six and a million homes were sprayed. In 1946, there were only seven officers on duty. Under Joseph Walter Mountin, the CDC continued to advocate for health issues. In 1947, the CDC made a payment of $10 to Emory University for 15 acres of land on Clifton Road in DeKalb County. CDC employees collected the money to make the purchase, the benefactor behind the “gift” was Robert W. Woodruff, chairman of the board of The Coca-Cola Company. Woodruff had a long-time interest in control, which had been a problem in areas where he went hunting. The same year, the PHS transferred its San Francisco based plague laboratory into the CDC as the Epidemiology Division, the mission of CDC expanded beyond its original focus on malaria to include sexually transmitted diseases when the Venereal Disease Division of the U. S. Public Health Service was transferred to the CDC in 1957, shortly thereafter, Tuberculosis Control was transferred to the CDC from PHS, and then in 1963 the Immunization program was established. It became the National Communicable Disease Center effective July 1,1967, the organization was renamed the Center for Disease Control on June 24,1970, and Centers for Disease Control effective October 14,1980. An act of the United States Congress appended the words and Prevention to the name effective October 27,1992, however, Congress directed that the initialism CDC be retained because of its name recognition. Currently the CDC focus has broadened to include chronic diseases, disabilities, injury control, workplace hazards, environmental health threats, and terrorism preparedness

4.
Taxonomy (biology)
–
Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate

5.
Bacterium
–
Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea

6.
Proteobacteria
–
The Proteobacteria are a major phylum of Gram-negative bacteria. The name of the phylum has never been published as no type genus has been proposed. They include a variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia. Others are free-living, and include many of the responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the purple bacteria, the Alphaproteobacteria grow at very low levels of nutrients and have unusual morphology such as stalks and buds. They include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants, the type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The Betaproteobacteria are highly diverse and contain chemolithoautotrophs, photoautotrophs. The type order is the Burkholderiales, comprising a range of metabolic diversity. The Gammaproteobacteria are the largest class in terms of species with validly published names, the type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter. The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp, the Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp, the type order is the Oligoflexales, which contains the genus Oligoflexus. The Acidithiobacillia contain only sulfur-oxidising autotrophs, the type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp. All Proteobacteria are Gram-negative, though some may stain Gram-positive or Gram-variable in practice, many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the Myxobacteriales, an order of bacteria that can aggregate to form fruiting bodies. Also, a variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, Chemolithoautotrophic, and heterotrophic, a variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. Proteobacteria are associated with the imbalance of microbiota of the reproductive tract of women

7.
Neisseriaceae
–
The Neisseriaceae are a family of Proteobacteria, within the Neisseriales order. As a group, the Neisseriaceae are strictly aerobic and Gram-negative, occur mainly in pairs, bacteria of Medical Importance in Todars Online Textbook of Bacteriology. CS1 maint, Multiple names, authors list Ryan KJ, Ray CG

8.
Binomial nomenclature
–
Such a name is called a binomial name, a binomen, binominal name or a scientific name, more informally it is also called a Latin name. The first part of the name identifies the genus to which the species belongs, for example, humans belong to the genus Homo and within this genus to the species Homo sapiens. The formal introduction of system of naming species is credited to Carl Linnaeus. But Gaspard Bauhin, in as early as 1623, had introduced in his book Pinax theatri botanici many names of genera that were adopted by Linnaeus. Although the general principles underlying binomial nomenclature are common to these two codes, there are differences, both in the terminology they use and in their precise rules. Similarly, both parts are italicized when a binomial name occurs in normal text, thus the binomial name of the annual phlox is now written as Phlox drummondii. In scientific works, the authority for a name is usually given, at least when it is first mentioned. In zoology Patella vulgata Linnaeus,1758, the original name given by Linnaeus was Fringilla domestica, the parentheses indicate that the species is now considered to belong in a different genus. The ICZN does not require that the name of the person who changed the genus be given, nor the date on which the change was made, in botany Amaranthus retroflexus L. – L. is the standard abbreviation used in botany for Linnaeus. – Linnaeus first named this bluebell species Scilla italica, Rothmaler transferred it to the genus Hyacinthoides, the ICN does not require that the dates of either publication be specified. Prior to the adoption of the binomial system of naming species. Together they formed a system of polynomial nomenclature and these names had two separate functions. First, to designate or label the species, and second, to be a diagnosis or description, such polynomial names may sometimes look like binomials, but are significantly different. For example, Gerards herbal describes various kinds of spiderwort, The first is called Phalangium ramosum, Branched Spiderwort, is aptly termed Phalangium Ephemerum Virginianum, Soon-Fading Spiderwort of Virginia. The Latin phrases are short descriptions, rather than identifying labels, the Bauhins, in particular Caspar Bauhin, took some important steps towards the binomial system, by pruning the Latin descriptions, in many cases to two words. The adoption by biologists of a system of binomial nomenclature is due to Swedish botanist and physician Carl von Linné. It was in his 1753 Species Plantarum that he first began using a one-word trivial name together with a generic name in a system of binomial nomenclature. This trivial name is what is now known as an epithet or specific name

9.
Gram-negative bacteria
–
Gram-negative bacteria are a group of bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are spread worldwide, in all environments that support life. Several classes of antibiotics target gram-negative bacteria specifically, including aminoglycosides, historically, the kingdom Monera was divided into four divisions based on Gram staining, Firmacutes, Gracillicutes, Mollicutes and Mendocutes. Since 1987, the monophyly of the bacteria has been disproven with molecular studies. However some authors, such as Cavalier-Smith still treat them as a monophyletic taxon, bacteria are traditionally divided into the two groups, gram-positive and gram-negative, based on their Gram stain retention. These groups are thought of as lineages, with gram-negative bacteria more closely related to one another than to gram-positive bacteria. While this is true, the classification system breaks down in some cases. A given bacterias Gram stain result, bacterial membrane organization, as such, the Gram stain cannot be reliably used to assess familial relationships of bacteria. That said, Gram staining does often give information about the composition of the cell membrane. Of these two distinct groups of prokaryotic organisms, monoderm prokaryotes are indicated to be ancestral. In addition, a number of taxa that are either part of the phylum Firmicutes or branches in its proximity are also found to possess a diderm cell structure. Other notable groups of bacteria include the cyanobacteria, spirochaetes, green sulfur. Medically relevant gram-negative cocci include the four types that cause a sexually transmitted disease, a meningitis, medically relevant gram-negative bacilli include a multitude of species. Some of them cause primarily respiratory problems, primarily urinary problems, transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation and transduction. In transformation, the material passes through the intervening medium. One of the unique characteristics of gram-negative bacteria is the structure of the bacterial outer membrane. The outer leaflet of this comprises a complex lipopolysaccharide whose lipid portion acts as an endotoxin

10.
Anaerobic organism
–
An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if oxygen is present, an anaerobic organism may be unicellular or multicellular. Van Leeuwenhoek sealed one of the tubes by using a flame. In 1913 Martinus Beijerinck repeated Van Leeuwenhoeks experiment and identified Clostridium butyricum as a prominent anaerobic bacterium in the sealed pepper infusion tube liquid. That Leeuwenhoek, one hundred years before the discovery of oxygen, for practical purposes, there are three categories of anaerobe, Obligate anaerobes, which are harmed by the presence of oxygen. Aerotolerant organisms, which use oxygen for growth, but tolerate its presence. Facultative anaerobes, which can grow without oxygen but use oxygen if it is present, some obligate anaerobes use fermentation, while others use anaerobic respiration. In the presence of oxygen, facultative anaerobes use aerobic respiration, without oxygen, some of them ferment, there are many anaerobic fermentative reactions. This is only 5% of the energy per molecule that the typical aerobic reaction generates. Since normal microbial culturing occurs in air, which is an aerobic environment. Hydrogen then reacts with oxygen gas on a palladium catalyst to more water. The issue with the Gaspak method is that a reaction can take place where the bacteria may die. The thioglycollate supplies a medium mimicking that of a dicot, thus providing not only an anaerobic environment, complex multicellular life that does not need oxygen is said to be rare, however there are examples of such organisms. Some organisms metabolise primarily using glycogen, for example the Nereid s and some polychaetes, or the juvenile Trichinella spiralis parasites. )

11.
Coccobacillus
–
A coccobacillus is a type of bacterium with a shape intermediate between cocci and bacilli. Coccobacilli, then, are very short rods which may be mistaken for cocci, haemophilus influenzae, Gardnerella vaginalis, and Chlamydia trachomatis are coccobacilli. Aggregatibacter actinomycetemcomitans is a Gram-negative coccobacillus prevalent in subgingival plaques, acinetobacter strains may grow on solid media as coccobacilli. Bordetella pertussis is a Gram-negative coccobacillus responsible for causing whooping cough, coxiella burnetti is also a coccobacillus. Bacteria from the Brucella genus are medically important coccobacilli that cause brucellosis, haemophilus ducreyi, another medically important Gram-negative coccobacillus, is observed in sexually transmitted disease, chancroid, of Third World countries. Pasteurellae are small, nonmotile, Gram-negative coccobacilli often exhibiting bipolar staining, in cattle, they cause life-threatening pneumonia. They are non-pathogenic for cats and dogs, as they are part of the normal nasopharyngeal flora, in humans, they cause chronic abscesses on the extremities or face following cat/dog bites

12.
Flagellum
–
A flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells. The word flagellum in Latin means whip, the primary role of the flagellum is locomotion, but it also often has function as a sensory organelle, being sensitive to chemicals and temperatures outside the cell. Flagella are organelles defined by function rather than structure, large differences occur between different types of flagella, the prokaryotic and eukaryotic flagella differ greatly in protein composition, structure, and mechanism of propulsion. However, both can be used for swimming, an example of a flagellated bacterium is the ulcer-causing Helicobacter pylori, which uses multiple flagella to propel itself through the mucus lining to reach the stomach epithelium. An example of a eukaryotic cell is the mammalian sperm cell. Eukaryotic flagella are structurally identical to eukaryotic cilia, although distinctions are made according to function and/or length. Fimbriae and pili are also thin appendages, but have different functions and are usually smaller, three types of flagella have so far been distinguished, bacterial, archaeal, and eukaryotic. The main differences among these three types are, Bacterial flagella are helical filaments, each with a motor at its base which can turn clockwise or counterclockwise. They provide two of several kinds of bacterial motility, archaeal flagella are superficially similar to bacterial flagella, but are different in many details and considered non-homologous. Eukaryotic flagella—those of animal, plant, and protist cells—are complex cellular projections that lash back, eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, and are not undulipodia, they have a structurally different 9+0 axoneme rather than the 9+2 axoneme found in both flagella and motile cilia undulipodia, the bacterial flagellum is made up of the protein flagellin. Its shape is a 20-nanometer-thick hollow tube and it is helical and has a sharp bend just outside the outer membrane, this hook allows the axis of the helix to point directly away from the cell. A shaft runs between the hook and the body, passing through protein rings in the cells membrane that act as bearings. Gram-positive organisms have two of these basal body rings, one in the layer and one in the plasma membrane. The filament ends with a capping protein, the flagellar filament is the long, helical screw that propels the bacterium when rotated by the motor, through the hook. Each protofilament is a series of protein chains. However, Campylobacter jejuni has seven protofilaments, the basal body has several traits in common with some types of secretory pores, such as the hollow, rod-like plug in their centers extending out through the plasma membrane. The bacterial flagellum is driven by an engine made up of protein

13.
Tarball (oil)
–
A tarball is a blob of petroleum which has been weathered after floating in the ocean. Tarballs are an aquatic pollutant in most environments, although they can occur naturally, tarball concentration and features have been used to assess the extent of oil spills and their composition can also be used to identify their sources of origin. Tarballs may be dispersed long distances by deep sea currents. The density of tarballs depends on the picked up in the weathering process. They can range in density with some being more dense than seawater, when the tarballs are less dense than seawater, they can travel over great distances. They can also be contained like oil and picked up using a variety of methods, containment booms can be used to isolate tarballs similar to methods used to isolate oil

14.
Trehalose
–
Trehalose, also known as mycose or tremalose, is a natural alpha-linked disaccharide formed by an α, α-1, 1-glucoside bond between two α-glucose units. Wiggers discovered trehalose in an ergot of rye, and in 1859 Marcellin Berthelot isolated it from trehala manna, a made by weevils. It can be synthesised by bacteria, fungi, plants, and it is implicated in anhydrobiosis — the ability of plants and animals to withstand prolonged periods of desiccation. It has high water retention capabilities, and is used in food, the sugar is thought to form a gel phase as cells dehydrate, which prevents disruption of internal cell organelles, by effectively splinting them in position. Rehydration then allows normal cellular activity to be resumed without the major, trehalose is not an antioxidant, because it is a non-reducing sugar and does not contain nucleophilic groups in its molecule. However, it was reported to have antioxidant effects, extracting trehalose was once a difficult and costly process, but circa the year 2000, the Hayashibara company confirmed an inexpensive extraction technology from starch for mass production. Trehalose is used in a spectrum of applications. Trehalose is a formed by a 1, 1-glucoside bond between two α-glucose units. Because trehalose is formed by the bonding of two reducing aldehyde groups, it has no capacity to participate in the Maillard reaction, there is an industrial process where trehalose is derived from corn starch. There are at least 3 biological pathways for trehalose biosynthesis, trehalose is a nonreducing sugar formed from two glucose units joined by a 1-1 alpha bond, giving it the name of α-D-glucopyranosyl--α-D-glucopyranoside. The bonding makes trehalose very resistant to hydrolysis, and therefore is stable in solution at high temperatures. The bonding also keeps nonreducing sugars in closed-ring form, such that the aldehyde or ketone end groups do not bind to the lysine or arginine residues of proteins, trehalose is less soluble than sucrose, except at high temperatures. Trehalose forms a crystal as the dihydrate, and has 90% of the calorific content of sucrose in that form. Anhydrous forms of trehalose readily regain moisture to form the dihydrate, anhydrous forms of trehalose can show interesting physical properties when heat-treated. Trehalose aqueous solutions show a concentration-dependent clustering tendency, owing to their ability to form hydrogen bonds between one another, they self-associate in water to form clusters of various sizes. Trehalose directly interacts with nucleic acids, facilitates melting of double stranded DNA,135 Trehalase deficiency is unusual in humans, except in the Greenlandic Inuit, where it occurs in 10%-15% of the population. p. 444 In nature, trehalose can be found in animals, plants, in animals, trehalose is prevalent in shrimp, and also in insects, including grasshoppers, locusts, butterflies, and bees, in which blood-sugar is trehalose. The trehalose is then broken down into glucose by the enzyme trehalase for use

15.
Gluconic acid
–
Gluconic acid is an organic compound with molecular formula C6H12O7 and condensed structural formula HOCH24COOH. It is one of the 16 stereoisomers of 2,3,4,5, in aqueous solution at neutral pH, gluconic acid forms the gluconate ion. The salts of gluconic acid are known as gluconates, gluconic acid, gluconate salts, and gluconate esters occur widely in nature because such species arise from the oxidation of glucose. Some drugs are injected in the form of gluconates, the chemical structure of gluconic acid consists of a six-carbon chain with five hydroxyl groups terminating in a carboxylic acid group. In aqueous solution, gluconic acid exists in equilibrium with the cyclic ester glucono delta-lactone, gluconic acid occurs naturally in fruit, honey, and wine. As a food additive, it is an acidity regulator and it is also used in cleaning products, where it dissolves mineral deposits, especially in alkaline solution. The gluconate anion chelates Ca2+, Fe2+, Al3+, and other metals, in 1929 Horace Terhune Herrick developed a process for producing the salt by fermentation. Gluconate is also a present in certain solutions, such as plasmalyte a. Quinine gluconate is a salt between gluconic acid and quinine, which is used for injection in the treatment of malaria. Zinc gluconate injections are used to neuter male dogs, ferrous gluconate injections have been proposed in the past to treat anemia. Gluconic acid on NIST. gov ChemSub Online, D-Gluconic acid

16.
Arabinose
–
Arabinose is an aldopentose – a monosaccharide containing five carbon atoms, and including an aldehyde functional group. For biosynthetic reasons, most saccharides are almost always more abundant in nature as the D-form, however, L-arabinose is in fact more common than D-arabinose in nature and is found in nature as a component of biopolymers such as hemicellulose and pectin. The L-arabinose operon, also known as the operon, has been the subject of much biomolecular research. The operon directs the catabolism of arabinose in E. coli, and it is activated in the presence of arabinose. A classic method for the synthesis of arabinose from glucose is the Wohl degradation. Arabinose gets its name from gum arabic, from which it was first isolated, in synthetic biology, arabinose is often used as a one-way or reversible switch for protein expression under the Pbad promoter in E. coli. This on-switch can be negated by the presence of glucose or reversed off by the addition of glucose in the medium which is a form of catabolite repression. Some organic acid tests check for the presence of arabinose, which may indicate overgrowth of intestinal yeast such as Candida albicans or other yeast/fungus species. Originally commercialized as a sweetener, arabinose is an inhibitor of sucrase and this inhibitory effect has been validated both in rodents and humans. Therefore, arabinose could be used in foods to attenuate the peak of glycemic response after the consumption of sucrose, the long-term effects of arabinose consumption on blood glucose parameters such as HbA1c and fasting blood glucose levels are unknown. Foods that contain arabinose are usually designed for prediabetic and diabetic patients and these foods are especially popular in Japan and China, where arabinose is legally used as a food additive. Arabinose is a prebiotic, because it cannot be absorbed by human intestine

17.
Maltose
–
Maltose, also known as maltobiose or malt sugar, is a disaccharide formed from two units of glucose joined with an α bond, formed from a condensation reaction. The isomer isomaltose has two glucose molecules linked through an α bond, maltose is the second member of an important biochemical series of glucose chains. Maltose is the disaccharide produced when amylase breaks down starch and it is found in germinating seeds as they break down their starch stores to use for food, which is why it was named after malt. It is also produced when glucose is caramelized, maltose was discovered by Irish chemist and brewer Cornelius OSullivan in 1872. Its name comes from malt, from Old English mealt, of Germanic origin, and the suffix –ose, maltose is a biomolecule that belongs to the group of carbohydrates within the division of biomolecules into the three main groups, carbohydrates, lipids and proteins. Carbohydrates are composed of carbon, oxygen and hydrogen C, O, H and are either polyhydroxyaldehydes or polyhydroxyketones, as a group, they are generally divided into monosaccharides, oligosaccharides, and polysaccharides depending on the number of sugar subunits. Maltose is an oligosaccharide, specifically a disaccharide, formed by the union of two glucose units, glucose is classified as a hexose because it is composed of six carbons. The link is characterized as α due to the O-glycosidic bond to the anomeric carbon being in the plane from the CH 2OH substituent in the same ring. If the O-glycosidic bond to the carbon was in the same plane as the CH 2OH substituent, it would be classified as a β bond. Due to O-glycosidic link, maltose is a disaccharide that can reduce Fehlings reagent, furthermore, maltose can be obtained by hydrolysis of glycogen or starch, polymers of linked maltoses in position α and branching in position α. These are very abundant and form a number of branches. Amylase enzymes produce maltose and limit dextrin and these can be further degraded by maltase enzyme to hydrolyze maltoses as glucoses and they are ready to be degrade and obtain energy in form of ATP. An isomer of maltose is isomaltose and this is similar to maltose but instead of bonds in position α, the linkage is formed in position α, therefore, glycogen branching is defined by isomaltose. maltose, isomaltose is also a reducing sugar. Maltose has the ability to reduce the Fehling’s solution, due to its free aldehyde, the aldehyde group is oxidized giving a positive result, which means that the maltose is a reducing sugar. Maltose in aqueous solution exhibit mutarotation, due to its anomeric carbon which can form α and β isomers, in aqueous solutions, it is in equilibrium between its α and β forms. It is sometimes water-soluble and sometimes crystalline, homopolysaccharides of glucose are broken down by maltase and isomaltase to produce glucose. The lack of the Sucrase-Isomaltase enzyme, one of the four integral glycoproteins and this congenital disorder is most prominent in infancy but can develop later in life. It is caused by an autosomal mutation

18.
Burkholderia pseudomallei
–
Burkholderia pseudomallei is a Gram-negative, bipolar, aerobic, motile rod-shaped bacterium. It is a soil-dwelling bacterium endemic in tropical and subtropical regions worldwide, particularly in Thailand and it infects humans and animals and causes the disease melioidosis. It is also capable of infecting plants, B. pseudomallei measures 2–5 μm in length and 0. 4–0.8 μm in diameter and is capable of self-propulsion using flagella. The bacteria can grow in a number of artificial nutrient environments, especially betaine-, in vitro, optimal proliferation temperature is reported around 40 °C in neutral or slightly acidic environments. The majority of strains are capable of fermentation of sugars without gas formation, bacteria produce both exo- and endotoxins. The role of the toxins identified in the process of melioidosis symptom development has not been fully elucidated, B. pseudomallei is not fastidious and grows on a large variety of culture media. Ashdowns medium may be used for selective isolation, cultures typically become positive in 24 to 48 hours. Colonies are wrinkled, have an appearance, and possess an earthy odour. On Gram staining, the organism is a Gram-negative rod with a safety pin appearance. On sensitivity testing, the organism appears highly resistant and that again differentiates it from B. mallei, for environmental specimens only, differentiation from the nonpathogenic B. thailandensis using an arabinose test is necessary. The laboratory identification of B. pseudomallei has been described in the literature, some suggest the Wayson stain is useful for this purpose, but this has been shown not to be the case. Laboratory identification of B. pseudomallei can be difficult, especially in Western countries where it is rarely seen, the large, wrinkled colonies look like environmental contaminants, so are often discarded as being of no clinical significance. Colony morphology is variable and a single strain may display multiple colony types. The organism grows more slowly than other bacteria that may be present in clinical specimens, nonsterile specimens should, therefore, be cultured in selective media. For heavily contaminated samples, such as faeces, a version of Ashdowns that includes norfloxacin, amoxicillin. In blood culture, the BacT/ALERT MB system by bioMérieux has been shown to have superior yields compared to conventional blood culture media. Again, because the disease is seen in Western countries. The pattern of resistance to antimicrobials is distinctive, and helps to differentiate the organism from P. aeruginosa, molecular methods of diagnosis are possible, but not routinely available for clinical diagnosis

19.
Aztreonam
–
Aztreonam is a monobactam antibiotic used primarily to treat infections caused by gram-negative bacteria. It is a drug based on a simpler monobactam isolated from Chromobacterium violaceum. It is resistant to some beta-lactamases, but is inactivated by extended-spectrum beta-lactamases and it was approved by the U. S. Food and Drug Administration in 1986. Aztreonam has strong activity against susceptible Gram-negative bacteria, including Pseudomonas aeruginosa and it has no useful activity against Gram-positive bacteria or anaerobes. It is known to be effective against a range of bacteria including Citrobacter, Enterobacter, E. coli, Haemophilus, Klebsiella, Proteus. The following represents MIC susceptibility data for a few medically significant microorganisms, furthermore, Aeromonas hydrophila, Citrobacter diversus, Enterobacter agglomerans, Haemophilus spp. and Streptococcus pyogenes have developed resistance to aztreonam to varying degrees. Aztreonam is often used in patients who are allergic or who cannot tolerate aminoglycosides. Aztreonam is poorly absorbed when given orally, so it must be administered as an intravenous or intramuscular injection, in the United States, the FDA approved the inhalation form on February 22,2010, for the suppression of P. aeruginosa infections in patients with cystic fibrosis. It received conditional approval for administration in Canada and the European Union in September 2009, reported side effects include injection site reactions, rash, and rarely toxic epidermal necrolysis. Gastrointestinal side effects include diarrhea and nausea and vomiting. However, like other beta lactams, there is a risk of serious allergic reactions. The aztreonam label directs physicians to be aware of the possibility of severe adverse reactions. This is more likely if the patient is allergic to a certain cephalosporin known as ceftazidime, azetreonam exhibits cross-reactivity with this cephalosporin due to a similar side chain. Physicians should evaluate prior allergy history when prescribing this medicine, special caution is warranted in patients who are allergic to ceftazidime and are subsequently placed on aztreonam therapy. Aztreonam is similar in action to penicillin and it inhibits mucopeptide synthesis in the bacterial cell wall, thereby blocking peptidoglycan crosslinking. It has a high affinity for penicillin-binding protein-3 and mild affinity for penicillin-binding protein-1a. Aztreonam binds the penicillin-binding proteins of Gram-positive and anaerobic bacteria very poorly and is ineffective against them. Aztreonam is bactericidal, but less so than some of the cephalosporins

20.
Aerobic bacteria
–
An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. In contrast, an organism is any organism that does not require oxygen for growth. Some anaerobes react negatively or even die if oxygen is present, obligate aerobes need oxygen to grow. In a process known as respiration, these organisms use oxygen to oxidize substrates. Facultative anaerobes use oxygen if it is available, but also have anaerobic methods of energy production, microaerophiles require oxygen for energy production, but are harmed by atmospheric concentrations of oxygen. Aerotolerant anaerobes do not use oxygen but are not harmed by it, a good example is the oxidation of glucose in aerobic respiration. C6H12O6 +6 O2 +38 ADP +38 phosphate →6 CO2 +6 H2O +38 ATP Oxygen is used during the oxidation of glucose and water is produced. This equation is a summary of what happens in three series of reactions, glycolysis, the Krebs cycle, and oxidative phosphorylation. Aerobic digestion Anaerobic digestion Fermentation Aerobic vaginitis Oxygenation

21.
Pseudomonas aeruginosa
–
Pseudomonas aeruginosa is a common Gram-negative, rod-shaped bacterium that can cause disease in plants and animals, including humans. A species of medical importance, P. The organism is considered opportunistic insofar as serious infection often occurs during existing diseases or conditions – most notably cystic fibrosis and it is also found generally in the immunocompromised but can infect the immunocompetent as in hot tub folliculitis. Treatment of P. aeruginosa infections can be due to its natural resistance to antibiotics. When more advanced antibiotic drug regimens are needed adverse effects may result and it is citrate, catalase, and oxidase positive. It is found in soil, water, skin flora, and it thrives not only in normal atmospheres, but also in low-oxygen atmospheres, thus has colonized many natural and artificial environments. It uses a range of organic material for food, in animals. The symptoms of infections are generalized inflammation and sepsis. If such colonizations occur in body organs, such as the lungs, the urinary tract, and kidneys. Because it thrives on moist surfaces, this bacterium is found on and in medical equipment, including catheters, causing cross-infections in hospitals. It is implicated in hot-tub rash and it is also able to decompose hydrocarbons and has been used to break down tarballs and oil from oil spills. P. aeruginosa does not fare well under suboptimal atmospheric conditions. The importance of the American cockroach as potential reservoirs or vectors of P. aeruginosa continues to be studied, the word Pseudomonas means false unit, from the Greek pseudo and. The stem word mon was used early in the history of microbiology to refer to germs, the species name aeruginosa is a Latin word meaning verdigris, referring to the blue-green color of laboratory cultures of the species. This blue-green pigment is a combination of two metabolites of P. aeruginosa, pyocyanin and pyoverdine, which impart the characteristic color of cultures. Another assertion is that the word may be derived from the Greek prefix ae- meaning old or aged, the names pyocyanin and pyoverdine are from the Greek, with pyo-, meaning pus, cyanin, meaning blue, and verdine, meaning green. Pyoverdine in the absence of pyocyanin is a fluorescent-yellow color and this set of genes is the P. aeruginosa core genome. P. aeruginosa is a facultative anaerobe, as it is adapted to proliferate in conditions of partial or total oxygen depletion

22.
Amoeba
–
An amoeba, often called amoeboid, is a type of cell or organism which has the ability to alter its shape, primarily by extending and retracting pseudopods. Amoebas do not form a taxonomic group, instead, they are found in every major lineage of eukaryotic organisms. Amoeboid cells occur not only among the protozoa, but also in fungi, algae, microbiologists often use the terms amoeboid and amoeba interchangeably for any organism that exhibits amoeboid movement. In older classification systems, most amoebas were placed in the class or subphylum Sarcodina, however, molecular phylogenetic studies have shown that Sarcodina is not a monophyletic group whose members share common descent. Consequently, amoeboid organisms are no longer classified together in one group, the best known amoeboid protists are the Giant Amoebae Chaos carolinense and Amoeba proteus, both of which are widely cultivated and studied in classrooms and laboratories. Amoebae move and feed by using pseudopods, which are bulges of cytoplasm formed by the action of actin microfilaments pushing out the plasma membrane that surrounds the cell. The appearance and internal structure of pseudopods are used to distinguish groups of amoebae from one another, amoebozoan species, such as those in the genus Amoeba, typically have bulbous pseudopods, rounded at the ends and roughly tubular in cross-section. Cercozoan amoeboids, such as Euglypha and Gromia, have slender, foraminifera emit fine, branching pseudopods that merge with one another to form net-like structures. Some groups, such as the Radiolaria and Heliozoa, have stiff, needle-like, free-living amoebae may be testate, or naked. The shells of testate amoebae may be composed of substances, including calcium, silica, chitin, or agglutinations of found materials like small grains of sand. To regulate osmotic pressure, most freshwater amoebae have a contractile vacuole which expels excess water from the cell and this organelle is necessary because freshwater has a lower concentration of solutes than the amoebas own internal fluids. Because the surrounding water is hypotonic with respect to the contents of the cell, without a contractile vacuole, the cell would fill with excess water and, eventually, burst. Marine amoebae do not usually possess a contractile vacuole, because the concentration of solutes within the cell are in balance with the tonicity of the surrounding water, the food sources of amoebae vary. Some amoebae are predatory and live by consuming bacteria and other protists, Some are detritivores and eat dead organic material. Amoebae typically ingest their food by phagocytosis, extending pseudopods to encircle, Amoeboid cells do not have a mouth or cytostome, and there is no fixed place on the cell at which phagocytosis normally occurs. Some amoebae also feed by pinocytosis, imbibing dissolved nutrients through vesicles formed within the cell membrane, the size of amoeboid cells and species is extremely variable. The marine amoeboid Massisteria voersi is just 2.3 to 3 micrometres in diameter, at the other extreme, the shells of deep-sea xenophyophores can attain 20 cm in diameter. Some multicellular organisms have amoeboid cells only in certain phases of life, in the immune system of humans and other animals, amoeboid white blood cells pursue invading organisms, such as bacteria and pathogenic protists, and engulf them by phagocytosis

23.
Trypanosomatida
–
This article is about the order Trypanosomatida, see also the genus Trypanosoma. Trypanosomatida is a group of kinetoplastid excavates distinguished by having only a single flagellum, the name is derived from the Greek trypano and soma because of the corkscrew-like motion of some trypanosomatid species. All members are exclusively parasitic, found primarily in insects, a few genera have life-cycles involving a secondary host, which may be a vertebrate, invertebrate or plant. These include several species that cause diseases in humans. The three major human diseases caused by trypanosomatids are, African trypanosomiasis, South American trypanosomiasis, the family is known from fossils of the extinct genus Paleoleishmania preserved in Burmese amber dating to the Albian and Dominican amber from the Burdigalian of Hispaniola. The genus Trypanosoma is also represented in Dominican amber in the extinct species Trypanosoma antiquus, there is one family in this order - Trypanosomatidae. Fifteen genera are recognised in the Trypanosomatidae and there are three subfamilies - Blechomonadinae, Leishmaniinae and Strigomonadinae, the subfamily Blechomonadinae has one genus - Blechomonas. The subfamily Leishmaniinae has three genera - Crithidia, Leishmania and Leptomonas, the subfamily Strigomonadinae also has three genera - Angomonas, Kentomonas and Strigomonas. The genera in the subfamily Strigomonadinae are characterised by the presence of intracellular bacteria, the other genera are Blastocrithidia, Herpetomonas, Jaenimonas, Paratrypanosoma, Phytomonas, Sergeia, Trypanosoma and Wallacemonas. Three genera are dixenous - Leishmania, Phytomonas and Trypanosoma and the remainder are monoxenous, Paratrypanosoma appears to be the first evolving branch in this order. Some trypanosomatids only occupy a single host, while others are heteroxenous. This heteroxenous life cycle includes the intestine of a bloodsucking insect. Rarer hosts include other bloodsucking invertebrates, such as leeches, different species go through a range of different morphologies at different stages of the life cycle, most have at least two different morphologies. Typically the promastigote and epimastigote forms are found in hosts, trypomastigote forms in the mammalian bloodstream. A variety of different morphological forms appear in the cycles of trypanosomatids, distinguished mainly by the position, length. The kinetoplast is found associated with the basal body at the base of the flagellum. Most of these morphologies can be found as a life stage in all trypanosomatid genera however certain morphologies are particularly common in a particular genus. Modern terminology is derived from the Greek, mastig, meaning whip, for example, the amastigote form is also known as the leishmanial form as all Leishmania have an amastigote life cycle stage

24.
Gram-positive bacteria
–
Gram-positive bacteria are bacteria that give a positive result in the Gram stain test. Gram-positive bacteria take up the crystal violet stain used in the test and this is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test. Their peptidoglycan layer is thinner and sandwiched between an inner cell membrane and a bacterial outer membrane, causing them to take up the counterstain. Despite their thicker peptidoglycan layer, gram-positive bacteria are more receptive to antibiotics than gram-negative, peptidoglycan chains are cross-linked to form rigid cell walls by a bacterial enzyme DD-transpeptidase. A much smaller volume of periplasm than that in gram-negative bacteria, only some species have a capsule usually consisting of polysaccharides. Also only some species are flagellates, and when they do have flagella they only have two basal body rings to support them, both gram-positive and gram-negative bacteria commonly have a surface layer called an S-layer. In gram-positive bacteria, the S-layer is attached to the peptidoglycan layer, specific to gram-positive bacteria is the presence of teichoic acids in the cell wall. Some of these are lipoteichoic acids, which have a component in the cell membrane that can assist in anchoring the peptidoglycan. Along with cell shape, Gram staining is a method used to differentiate bacterial species. Historically, the kingdom Monera was divided into four divisions based primarily on Gram staining, based on molecular studies of the 16S sequences, Woese recognised twelve bacterial phyla. Two of these were both gram-positive and were divided on the proportion of the guanine and cytosine content in their DNA, the high G + C phylum was made up of the Actinobacteria and the low G + C phylum contained the Firmicutes. The Actinobacteria include the Corynebacterium, Mycobacterium, Nocardia and Streptomyces genera, the Firmicutes, have a 45–60% GC content, but this is lower than that of the Actinobacteria. The gram-positive and gram-negative staining response is not a reliable characteristic as these two kinds of bacteria do not form phylogenetic coherent groups. All gram-positive bacteria are bounded by a lipid membrane, and, in general. For the bacterial cells bounded by a cell membrane, the term monoderm bacteria or monoderm prokaryotes has been proposed. The presence of inner and outer cell membranes defines a new compartment in these cells and these bacteria have been designated as diderm bacteria. The distinction between the monoderm and diderm bacteria is supported by conserved signature indels in a number of important proteins, of these two structurally distinct groups of bacteria, monoderms are indicated to be ancestral. In general, gram-positive bacteria are monoderms and have a lipid bilayer whereas gram-negative bacteria are diderms and have two bilayers

25.
Pefloxacin
–
Pefloxacin is a quinolone drug used to treat bacterial infections. Pefloxacin has not been approved for use in the United States, pefloxacin was developed in 1979 and approved in France for human use in 1985. Bacterial infections in the gastrointestinal system, however this indication is no longer effective due to bacterial resistance. Pefloxacin has been used as a veterinary medicine to treat microbial infections. Pefloxacin is an antibiotic that is active against both Gram-positive and Gram-negative bacteria. It functions by inhibiting DNA gyrase, a type II topoisomerase, and topoisomerase IV, tendinitis and rupture, usually of the Achilles tendon, are a class-effects of the fluoroquinolones, most frequently reported with pefloxacin. How Stuff Works - Cipro Package insert information

26.
Trimethoprim/sulfamethoxazole
–
Trimethoprim/sulfamethoxazole, also known as co-trimoxazole among other names, is an antibiotic used to treat a variety of bacterial infections. It consists of one part trimethoprim to five parts sulfamethoxazole and it is used for urinary tract infections, MRSA skin infections, travelers diarrhea, respiratory tract infections, and cholera, among others. It may be used both to treat and prevent pneumocystis pneumonia in people with HIV/AIDS and it can be given by mouth or intravenously. Common side effects include nausea, vomiting, rash, and diarrhea, severe allergic reactions and Clostridium difficile diarrhea may occasionally occur. Its use near the end of pregnancy is not recommended and it appears to be safe for use during breastfeeding as long as the baby is healthy. TMP/SMX generally results in bacterial death and it works by blocking the making of folate by the bacteria. TMP/SMX was first sold in 1974 and it is on the World Health Organizations List of Essential Medicines, the most effective and safe medicines needed in a health system. It is available as a medication and is not very expensive. In the United States it is about 0.40 USD per dose, co-trimoxazole was claimed to be more effective than either of its components individually in treating bacterial infections, although this was later disputed. Co-trimoxazole in retinochoroiditis shows a reduction in the risk of recurrent retinochoroiditis, the global problem of advancing antimicrobial resistance has led to a renewed interest in the use of co-trimoxazole more recently. Organisms against which co-trimoxazole can be effective include, The only notable nonsusceptible organisms are the mycoplasmae and its use during pregnancy is contraindicated, although it has been placed in Australian and American pregnancy category C. Its use later on during pregnancy increases the risk of preterm labour. Animal studies have yielded similarly discouraging results and it is also excreted in breast milk and hence nursing during treatment with co-trimoxazole is generally advised against. A significant risk of megaloblastic anaemia exists with doses of pyrimethamine in excess of 25 mg/wk, antivirals, more specifically, lamivudine, zalcitabine and zidovudine Procainamide and/or amantadine may have their plasma concentrations increased bilaterally or unilaterally. Spironolactone — concurrent use can increase the likelihood of hyperkalemia, especially in the elderly, the trimethoprim portion acts to prevent potassium excretion in the distal tubule of the nephron. Potassium aminobenzoate — effects of sulfonamides inhibited, the synergy between trimethoprim and sulfamethoxazole was first described in the late 1960s. Trimethoprim and sulfamethoxazole have an effect when given together than when given separately. Sulfamethoxazole, a sulfonamide, induces its effects by interfering with the de novo synthesis of folate inside microbial organisms such as protozoa, fungi

27.
Penicillins
–
Penicillin is a group of antibiotics which include penicillin G, penicillin V, procaine penicillin, and benzathine penicillin. Penicillin antibiotics were among the first medications to be effective against many bacterial infections caused by staphylococci and streptococci, penicillins are still widely used today, though many types of bacteria have developed resistance following extensive use. About 10% of people report that they are allergic to penicillin, however, serious allergies only occur in about 0. 03%. Penicillin was discovered in 1928 by Scottish scientist Alexander Fleming, people began using it to treat infections in 1942. There are several enhanced penicillin families which are effective against additional bacteria, these include the penicillins, aminopenicillins. They are derived from Penicillium fungi, the term penicillin is often used generically to refer to benzylpenicillin, procaine benzylpenicillin, benzathine benzylpenicillin, and phenoxymethylpenicillin. Procaine penicillin and benzathine penicillin have the same activity as benzylpenicillin. Phenoxymethylpenicillin is less active against gram-negative bacteria than benzylpenicillin, infrequent adverse effects include fever, vomiting, erythema, dermatitis, angioedema, seizures, and pseudomembranous colitis. About 10% of people report that they are allergic to penicillin, however, serious allergies only occur in about 0. 03%. Penicillin can also induce serum sickness or a serum sickness-like reaction in some individuals, serum sickness is a type III hypersensitivity reaction that occurs one to three weeks after exposure to drugs including penicillin. It is not a drug allergy, because allergies are type I hypersensitivity reactions. Pain and inflammation at the site is also common for parenterally administered benzathine benzylpenicillin, benzylpenicillin. Significantly, there is a reaction to Streptolysin S, a toxin released by certain killed bacteria and associated with Penicillin injection. Allergic reactions to any β-lactam antibiotic may occur in up to 1% of patients receiving that agent, the allergic reaction is a Type I hypersensitivity reaction. Anaphylaxis will occur in approximately 0. 01% of patients and it has previously been accepted that there was up to a 10% cross-sensitivity between penicillin-derivatives, cephalosporins, and carbapenems, due to the sharing of the β-lactam ring. Assessments in 2006 found no risk for cross-allergy for second-generation or later cephalosporins than the first generation. However, as a risk, research shows that all beta lactams have the intrinsic hazard of very serious hazardous reactions in susceptible patients. Only the frequency of these reactions vary, based on the structure, bacteria constantly remodel their peptidoglycan cell walls, simultaneously building and breaking down portions of the cell wall as they grow and divide

28.
Carbapenem
–
Carbapenems are antibiotics used for the treatment of infections known or suspected to be caused by multidrug-resistant bacteria. Their use is primarily in people who are hospitalized, like the penicillins and cephalosporins, they are members of the beta lactam class of antibiotics, which kill bacteria by binding to penicillin-binding proteins and inhibiting cell wall synthesis. They exhibit a spectrum of activity compared to cephalosporins and penicillins. Their effectiveness is less affected by many mechanisms of antibiotic resistance than other beta lactams. Carbapenem antibiotics were developed at Merck & Co. from the carbapenem thienamycin. Concern has arisen in recent years over increasing rates of resistance to carbapenems, agents with anti-pseudomonal activity, including doripenem, imipenem, and meropenem are not recommended in this population. Doripenem, imipenem, and meropenem are recommended for high-risk community-acquired abdominal infections, combination therapy, typically with an aminoglycoside, is recommended for Pseudomonas infections to avoid resistance development during treatment. Imipenem and meropenem are useful in cases in which P. aeruginosa is a suspected pathogen, in 2015, the National Institute for Health and Care Excellence recommended piperacillin-tazobactam as first line therapy for the treatment of bloodstream infections in neutropenic cancer patients. For bloodstream infections known to be due to extended spectrum beta-lactamase producing Enterobacteriaceace, carbapenems exhibit broad spectrum activity against gram-negative bacteria and somewhat narrower activity against gram-positive bacteria. For empiric therapy they are combined with a second drug having broader spectrum gram-positive activity. Activity is maintained against most strains of E. coli and K. pneumoniae that are resistant to cephalosporins due to the production of extended spectrum beta-lactamases, imipenem, doripenem, and meropenem also exhibit good activity against most strains of Pseudomonas aeruginosa and Acinetobacter species. The observed activity against these pathogens is especially valued as they are resistant to many other antibiotic classes. The spectrum of activity of the carbapenems against gram-positive bacteria is fairly broad, good activity is seen against methicillin-sensitive strains of Staphylococcus species, but many other antibiotics provide coverage for such infections. Good activity is observed for most Streptococcus species, including penicillin-resistant strains. Carbapenems generally exhibit good activity against anaerobes such as Bacteriodes fragilis, like other beta lactam antibiotics, they lack activity against atypical bacteria, which do not have a cell wall and are thus not affected by cell wall synthesis inhibitors. Carbapenems are contraindicated in patients with allergic reactions to beta lactam antibiotics. Serious and occasionally fatal allergic reactions can occur in people treated with carbapenems, seizures are a dose-limiting toxicity for both imipenem and meropenem. Clostridium difficile-related diarrhea may occur in people treated with carbapenems or other broad spectrum antibiotics, imipenem, the first clinically used carbapenem, was developed at Merck and Co

29.
Meropenem
–
Meropenem is an ultra-broad-spectrum antibiotic used to treat a wide variety of infections. It is a β-lactam and belongs to the subgroup of carbapenems, meropenem was developed by Dainippon Sumitomo Pharma and patented in 1983. It gained US FDA approval in July 1996 and it penetrates well into many tissues and body fluids, including cerebrospinal fluid, bile, heart valve, lung, and peritoneal fluid. It was initially marketed by AstraZeneca under the trade name Merrem, the spectrum of action includes many Gram-positive and Gram-negative bacteria and anaerobic bacteria. The overall spectrum is similar to that of imipenem, although meropenem is more active against Enterobacteriaceae and it works against extended-spectrum β-lactamases, but may be more susceptible to metallo-β-lactamases. Meropenem is frequently given in the treatment of febrile neutropenia and this condition frequently occurs in patients with hematological malignancies and cancer patients receiving anticancer drugs that suppress bone marrow formation. It is approved for complicated skin and skin infections, complicated intra-abdominal infections. Meropenem is administered intravenously as a crystalline powder to be dissolved in 5% monobasic potassium phosphate solution. Dosing must be adjusted for altered kidney function and for haemofiltration, the most common adverse effects are diarrhea, nausea and vomiting, injection-site inflammation, headache, rash and thrombophlebitis. Many of these effects were observed in severely ill individuals already taking many medications including vancomycin. One study showed Clostridium difficile-associated diarrhea happened in 3. 6% of meropenem patients, meropenem has a reduced potential for seizures in comparison with imipenem. Several cases of severe hypokalemia have been reported, meropenem, like other carbopenems, is a potent inducer of multidrug resistance in bacteria. Meropenem is bactericidal except against Listeria monocytogenes, where it is bacteriostatic and it inhibits bacterial wall synthesis like other β-lactam antibiotics. In contrast to other beta-lactams, it is resistant to degradation by β-lactamases or cephalosporinases. In general, resistance arises due to mutations in penicillin-binding proteins, production of metallo-β-lactamases, unlike imipenem, it is stable to dehydropeptidase-1, so can be given without cilastatin. In 2016 a synthetic peptide-conjugated PMO was found to inhibit the expression of New Delhi Metallo-beta-lactamase, an enzyme that many drug-resistant bacteria use to destroy carbapenems

30.
Base pair
–
A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must also be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5 end to the 3 end, thus and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature

31.
Open reading frame
–
In molecular genetics, an open reading frame is the part of a reading frame that has the potential to be translated. An ORF is a stretch of codons that do not contain a stop codon. An ATG codon within the ORF may indicate where translation starts, the transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, a protein would be made during translation. In eukaryotic genes with multiple exons, ORFs span intron/exon regions, one common use of closed reading frames is as one piece of evidence to assist in gene prediction. Long ORFs are often used, along with evidence, to initially identify candidate protein-coding regions or functional RNA-coding regions in a DNA sequence. The presence of an CRF does not necessarily mean that the region is never translated, for example, in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons. By itself even an open reading frame is not conclusive evidence for the presence of a gene. On the other hand, it has proven that some short ORFs that lack the classical hallmarks of protein-coding genes can produce functional peptides. 5’NTR of about 50% of mammal mRNAs are known to one or several sORFs. 64-75% of experimentally found translation initiation sites of sORFs are conservative in the genomes of human, such kind of situation is characteristic of SLAMF1 gene, for example. Since DNA is interpreted in groups of three nucleotides, a DNA strand has three reading frames. The double helix of a DNA molecule has two anti-parallel strands so, with the two strands having three reading frames each, there are six possible frame translations. ORF Finder, The ORF Finder is an analysis tool which finds all open reading frames of a selectable minimum size in a users sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes, the deduced amino acid sequence can be saved in various formats and searched against the sequence database using the BLAST server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions and it is also packaged with the Sequin sequence submission software. The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, the pairwise global alignment between the sequences makes it convenient to detect the different mutations, including single nucleotide polymorphism. Needleman and Wunsch algorithms are used for the gene alignment, the ORF Investigator is written in the portable Perl programming language, and is therefore available to users of all common operating systems

32.
PubMed Identifier
–
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby

Longitudinal section through the flagella area in Chlamydomonas reinhardtii. In the cell apex is the basal body that is the anchoring site for a flagellum. Basal bodies originate from and have a substructure similar to that of centrioles, with nine peripheral microtubule triplets (see structure at bottom center of image).

Example of a six-frame translation. The nucleotide sequence is shown in the middle with forward translations above and reverse translations below. Two possible open reading frames with the sequences are highlighted.